Abiotic stress is one of the most important factors in reducing crop yield. Eukaryotic initiation factor (eIF) virtually regulates cellular activities and signaling in eukaryotic systems; it has been reported in monocotyledonous plants, however, its role in dicotyledonous plant adversity stress remains scarce. Here, we identified GmseIF2B5 gene and created the editing lines ( sp1 and sp4) by CRISPR/Cas9 technology in soybean. sp1 and sp4 lines boost tolerance to drought stress; RNA sequence analysis revealed that the differential gene was significantly enriched in the phenylpropanoid biosynthesis metabolic pathway; GmeIF2B5 interacts with GmPOD4 in vitro and in vivo, which encodes peroxidase, the last enzyme that catalyzes lignin synthesis. In addition, sp1 and sp4 lines also improved salt tolerance in soybean by increasing peroxidase activity and balancing Na +/K + ratio. Intriguingly, gmeif2b5 single and eif2b5pod4 double gene-edited lines both enhanced tolerances to salt and drought stress. Collectively, the findings reveal that the GmeIF2B5-GmPOD4 module mediates drought tolerance through lignin biosynthesis and increases salt tolerance by balancing the Na +/K + ratio in soybeans. The discovery fills the role of eIF-like genes in soybeans, and it provides an avenue for the genetic improvement of salt- and drought-tolerant soybean varieties.